Thursday, May 31, 2012

Satellite imagery isn’t just for evading traffic jams and admiring your house from space. Peter Fretwell and his colleagues from the British Antarctic Survey, University in Minnesota, Scripps Institute of Oceanography and the Australian Antarctic Division used satellites to count Emperor penguins.

Emperor penguins (Aptenodytes fosteri) breed each year on the Antarctic sea ice. Until now, only five out of dozens of colonies have been regularly monitored. Therefore, conservationists have been able to make only rudimentary estimates as to the total number of birds. The best guess was that there were 135,000 to 175,000 breeding pairs. Fretwell and his associates felt they could do much better with satellites.

Emperor penguins offer the aspiring wildlife imager a number of advantages. For one thing, they’re large animals, reaching well over a meter in height. More importantly, they live in a barren monochromatic landscape where anything that’s not white is likely to be a penguin, a penguin’s shadow, or a penguin’s guano. With a bit of fiddling, researchers were able to distinguish between those three things well enough to get a fairly accurate bird count.

So, how many Emperor penguins were there? In 2009, the year of the study, the researchers estimated that there were close to 300,000 breeding pairs, at least twice as many as previously thought and very good news for the penguins. Unfortunately, with the diminishing of the sea ice due to climate change, the penguins probably won’t be able to enjoy those large numbers for long.

Wednesday, May 30, 2012

One of my peeves is that fantasy and science fiction books are often listed together. I find it frustrating to have to weed out wizards and vampires when I'm looking for a new book or series to read. If you feel the same way (or the opposite way), you may find this chart helpful. Go to the link to magnify and move around.

Tuesday, May 29, 2012

The International Institute for Species Exploration sorts
through the hundreds of species that are discovered each year to bring you
their top ten list. Species can be nominated for this great honor by
researchers or by the public, but the ultimate choice is made by the Top 10
International Committee, this year chaired by Mary Jameson of Wichita State
University.

Astute observers will notice that it bears a striking
resemblance to a sponge. Even more astute observers will see that it bears the
scientific name of Spongiforma squarepantsii. In case that’s not clear enough, the common name of this fungus is the ‘Spongebob Squarepants Mushroom’. For some reason, journal editors originally
rejected this name choice. Luckily, they came to their senses.

My second favorite species on the list is the Bonaire Banded
Box Jelly (Tamoya Ohboya), a beautiful
but deadly box jelly.

Photo credit: Ned DeLoach.

The public was invited to submit suggestions for its name,
and the winning selection was provided by high school biology teacher Lisa
Peck. Apparently, a lot of people associate ‘oh boy’ with encountering box
jellies.

You
can see the entire list here, as well as winners from previous years.

Monday, May 28, 2012

Just when you thought Mars rovers couldn’t get any cooler,
here comes the ‘tumbleweed rover’. As the name implies, this is a rover that
would travel across the Martian landscape driven solely by wind power. You can
see an artist’s rendition of such a rover below.

Credit: North Carolina State University.

Because conditions on Mars are unlike anything that can be
found on Earth, designing such a rover requires computer models and
simulations. Alexandre Hartl and Andre Mazzoleni of North Carolina State
University created their own simulations of Martian rock fields and wind
patterns to virtually test various
types of rovers.

The researchers compared rovers of different
sizes and weights to determine the optimal design. Not
surprisingly, lightweight rovers with large diameters were able to travel the
furthest in the same amount of time under the same wind conditions. This is
partly because they present a larger surface area to the wind, and partly
because larger rovers can more easily bounce over obstacles.
Perhaps most importantly, larger rovers don’t require as much wind to dislodge
them from behind rock formations or to get them going again once they’ve stalled.

The obvious advantage of using a tumbleweed rover is that it
would not expend any energy traveling from place to place. It could
therefore save all its power for sample collection, data analysis,
communication with Earth and other tasks. In addition, such a rover could
potentially travel great distances from its landing site over a variety of
terrains.

The obvious disadvantage is that the rover might never
happen to reach those regions of greatest interest to areologists. Remember,
there is no way to steer these rovers. Still, the much lower cost of these
lightweight rovers could allow for hordes of the devices to be deployed with
the hope that they would eventually spread across the planet.

By the way, if you pictured these rovers sedately rolling
along, you have the wrong image in your mind. They would most likely spend more time bouncing than rolling.

Sunday, May 27, 2012

We all want our schools to be safe for both
kids and teachers. The question is, how do you achieve that goal? In an effort
to make schools safer, many regions have adopted ‘zero tolerance’ policies that
require automatic suspension no matter the circumstances of the transgression.
Is this a good idea? According to my own common sense, the answer is a
resounding ‘no’. However, scientists should never trust common sense. We insist
on evidence. Luckily, Dewey Cornell of the University of Virginia, Korrie Allen
of Eastern Virginia Medical School and Xitao Fan from the University of Macau
have provided some.

The researchers
compared two different strategies for dealing with threats of violence. For one group of kids, school officials followed the Virginia Student Threat Assessment Guidelines.
According to these guidelines, administrators lead a team
of adults, including parents and at least one school psychologist, through a
series of interviews with the child who had made the threat. Based on their
findings, the team could consider the matter resolved right then or proceed with
further action, including suspension.

Kids in the second group were simply suspended from school as per the zero tolerance rules.

The kids in the
first group were significantly less likely to be referred for subsequent
offenses. They were more likely to receive mental health counseling. Their
classmates reported less overall bullying. Parents were more involved. And
perhaps most important, none of the original threats that had set the whole process in motion were carried out.

There is plenty of room for improvement in how schools handle threats of
violence. Different training programs for teachers and administrators may yield
different results. The community at large can be included to a greater or
lesser extent. However, one thing
seems clear. If the goal is to help kids safely negotiate their way through
school (and by extension, through later life) rather than simply to punish or
retaliate, incidents must be evaluated on a case by case basis. Zero tolerance
has no place in such a system.

Saturday, May 26, 2012

We all want to know whether water
is safe to swim in, and even more importantly, safe to drink. Unfortunately,
standard tests for bacterial contamination can take days. Luckily, those long
waits may be a thing of the past. Researchers from McMaster University have
developed a quick and easy test for E. coli.

The scientists used a new version
of bioactive paper, the little strips that, among other things, are used to
detect glucose in urine. While there are paper strips that detect bacteria, they
aren’t nearly sensitive enough. Bacterial counts are measured in colony-forming units per milliliter of water (cfu/mL). Currently available paper assays can only detect from 104 to 107 cfu/mL. The safe limit
for recreational water (water used for swimming or bathing) is less than five
cfu/mL. For drinking water, the limit is zero cfu/mL. In other words, to be
useful, such a test would need to be about a million times more sensitive.

In order to approach this level of
sensitivity, the researchers coated their bioactive papers with substrates that
change color in the presence of enzymes produced by E. coli. These chemicals can be layered onto the paper using an
ordinary inkjet printer. You then add a
lysing agent (a chemical which not only kills cells but effectively blows them up so that their enzymes are exposed to the outside) to your water sample, and apply the result to the
paper.

With this new method, it took only
a few minutes to detect five cfu/mL of E. coli. By placing
the water sample in growth media for a few hours, and thus allowing any
bacteria present to replicate, the authors were able to tell whether a single
bacterial cell had been in the original sample.

The same bioactive papers
successfully calibrated bacterial counts in milk, orange juice and on heads of
lettuce. As an added bonus, the reagents embedded in the papers remained stable
at room temperature for at least two months. In short, these new bioactive
papers are cheap, easy to use and easy to store.

Friday, May 25, 2012

You’ve heard of using leeches for bloodletting, a practice
that is making a comeback for a few specific conditions. Well, that’s not all
leeches are good for. Ida Bærholm Schnell and Philip Thomsen and their
colleagues from the University of Copenhagen and the University of Cambridge
have been using the little parasites to catalogue endangered species.

It’s exceedingly difficult to monitor rare mammals in remote
regions because, well, the animals are rare and the regions are remote. Unlike
humans, leeches seem to have no trouble finding mammals. Thanks to modern
sequencing techniques, mammalian DNA can be extracted from leeches after their
last blood meal. What makes leeches particularly useful is that fact that they
store this meal for many months.

After successfully testing the extraction of goat DNA from
leeches killed four months after their last meal, the scientists left the lab
and set out to collect leeches from the dense forests of the Central Annamite
region of Vietnam. Almost all the captured leeches (21 our of 25) contained
mammalian DNA. Six different mammals had donated their blood to the leeches, two of which had only recently been described
and two others of which were considered ‘threatened’.

Leeches come to you with the blood
samples, rather than you tracking down the animals in the jungle. Simple and
cheap, and the sampling does not require specially trained scientists, but can
be carried out by local people. I am convinced that this technique will
revolutionize the monitoring of threatened wildlife in rainforest habitats.

Why is this interesting? For
one thing, a very successful method of finding exoplanets is the ‘transit
method’. This method relies on the fact that the light coming from a distant
star will dim ever so slightly as one of its planets passes in front of it.
Watching a known transit close to home will give astronomers more confidence in
the advantages and limitations of this method. The only planets that can pass
in front of the sun from our perspective are Mercury and Venus. The other
planets would see Earth transit the sun, not the other way around. Therefore,
there are limited opportunities to observe a confirmed transit.

For people on Earth to see a
transit, the plane of Venus’s orbit has to cross that of the Earth’s.
Otherwise, Venus will appear either above or below the sun in our sky. This
occurs in a repeatable pattern with 12, 105-121, 12, 105-121 etc. years between
each event. The last Venus transit was twelve years ago in 2004.
This means that there won’t be another such event for over a century. Unless
drastic changes occur in the science of longevity, you won’t have another chance
to see a Venus transit.

Transits are also of historical significance. In the
eighteenth century, astronomers used the timing of a transit to determine the exact distance from the Earth to the sun. The
square of the time it takes a planet to orbit the sun (its period, or year) is
proportional to the cube of the radius of the orbit (distance from the planet
to the sun). Back then, astronomers knew the periods of Venus, and of course,
of the Earth. They could use measurements of the timing of Venus’s transit as
seen from different places on Earth to determine the
distance from Earth to Venus, and plug that in to get the distance to the sun. In fact, timing Venus’s transit was the mission
that had originally sent Captain Cook to the Fiji Islands in 1769.

Jay M Pasachoff, an astronomer at
Williams College, will be among those studying the transit next week. He writes:

For the upcoming transit of
Venus this June we want to get the most complete set of data possible, so that
the astronomers of 2117 will think that their forebears way back in 2012 did a
fine job even with their relatively primitive instruments.

I admire his combination of pride and humility as well as his faith in the future.

You can find more information about the transit of Venus here. It
includes a map of when Venus will cross the sun as seen from your location and
a link to download an app so you can send in your own transit observations. It
also describes how to safely observe the sun.

Of course, you can always let the folks at NASA do the
observing for you. They’re going to have a live ustream channel broadcasting
the transit. The folks at Astronomers Without Borders are also putting out information on the transit.

Wednesday, May 23, 2012

Each year, the Vision Sciences Society holds a contest for the best optical illusions. This year's Illusion of the Year, by Roger Newport, Helen Gilpin and Catherine Preston of the University of Nottingham, is 'The Disappearing Hand Trick', seen below.

Tuesday, May 22, 2012

About 10%
of people are left-handed, and this has held true for millennia. What’s maintaining that delicate
balance? Daniel Abrams and Mark Panaggio of Northwestern University created a mathematical model to answer that question.

It turns out
that it’s the amount of cooperation and competition in societies that
determines the degree of left-handedness. In a culture that is entirely
cooperative, no competition at all, being left-handed would be a definite
disadvantage for both the individual and the tribe. The left-handed person
can’t use the same tools as everyone else or can’t use them as well, leading
to slower overall work or the need to create specialty items just for him.

On the other
hand, in a highly competitive society, unusually-handed people would have an
edge. For example, in a world where the majority of people are right-handed, and thus are used to fighting other right-handed people, left-handed
combatants are more difficult to defeat. Lefties should outcompete righties until
the lefties stopped being the minority, then the advantage should shift. Thus, highly competitive groups should have a 50-50 ratio of right to left-handedness.

So, how well
does this model fit the real world? As I mentioned, in our relatively
cooperative society, left-handers have made up roughly 10% of the population
for the past 5,000 years. However, in the highly competitive world of sports,
that number is closer to 50%. In fact, more than 50% of the top baseball
players are lefties.

Abrams and
Panaggio claim that they can use their model to predict the percentage of
southpaws in any group, even non-human groups that display handedness like
parrots. If their model is true, it suggests that human societies are much more
cooperative than people give them credit for.

Monday, May 21, 2012

Dung beetles are
essential groundskeepers in many ecosystems. While many of them stereotypically roll dung into balls and
cartwheel away with their plunder, others bury the dung where it lies. The
feces may serve as food and shelter for the adults or as nurseries and larders
for their offspring. You might think that an animal that eats poo isn't going to be particularly picky, but science is all about testing ideas. To that end, Sean Whipple and Wyatt
Hoback of the University of Nebraska decided to find out if the beetles
displayed any particular preference for the dung of specific types of 'donors'.

To answer this
question, the researchers baited pitfall traps in the Nebraskan plains with
dung from a variety of native and exotic animals. Herbivores, carnivores and
omnivores were all well represented. Over the next two years, over 9000 dung
beetles from 15 different species were captured in the traps. I really want to
say that the researchers doo-doo-fully checked their traps, but I believe
they’ve suffered enough for science.

They found a few
interesting things. For one thing, these Nebraskan beetles did not prefer
native Nebraskan species such as bison, but were perfectly content to munch on
zebra or donkey manure. Closely related beetle species did not necessarily
prefer the same kind of feces. Overall, the beetles showed a marked
preference for omnivore dung, probably because it was the smelliest. Among the most highly coveted types of feces were those deposited by humans.

Sunday, May 20, 2012

Scoliosis is a disorder which causes the spine to curve sideways. In severe cases, it must be corrected surgically by attaching rods to straighten the spine. Unfortunately, as treatment often occurs during childhood, using fixed bracing rods can prevent normal spinal growth. Extendable rods are a big improvement, but they require surgical procedures every few months to mechanically lengthen them. Kenneth Man-Chee Cheung and his colleagues from the University of Hong Kong had a better idea. They used magnetically controlled growing rods (MCGR) to treat their young patients.

MCGRs are surgical rods that contain an extendable region with an internal magnet. The researchers implanted the MCGRs into five patients, all of whom were still actively growing. Each child was reevaluated every month, during which his or her rod was nonsurgically extended using an external magnet. Thus far, two of the patients have been observed for a full two years. The technique compares favorably with traditional growing rods but has several advantages. First, MCGRs do not require surgical procedures to extend them, greatly reducing the risk of infection, not to mention the pain of additional surgeries. Second, because extensions can occur much more frequently (doctors are loathe to operate on children more than twice a year), normal spinal growth can be much more closely approximated.

Needless to say, a sample size of two doth not a scientific consensus make. However, the preliminary results suggest that this technique is well worth further study. By the way, this is not the first time magnetic prosthetics have been used. Two years ago, I wrote about a similar technique used to lengthen a little girl’s leg.

Saturday, May 19, 2012

Although we don’t display social status the same way other primates do, many of the same physiological reactions apply. Having a low position in any primate hierarchy is associated with chronic stress and poor health. Researchers from the University of Chicago, Emory University, Johns Hopkins and the University of Vermont have found that the social status of female rhesus monkeys even affects gene expression. Correlations between gene expression and status have long been described, but efforts to prove causation have been problematic.

The scientists were able to control the social rank of the monkeys by manipulating the order in which new members were introduced into a small group. Blood tests revealed that certain genes were expressed at different levels, depending on the status of the monkey. For example, genes involved in immune reactions were expressed at a higher rate in high status females. In fact, when given blood samples, researchers were able to predict with 80% accuracy where a monkey fell within a hierarchy of five group mates. This was true even when the same unfortunate females were moved from group to group, changing status position each time. In other words, gene expression can change from moment to moment depending on where the individual finds herself ranked among her peers.

These data indicate that it is rank that influences gene expression and not the other way around. If gene expression came first, monkeys would not necessarily change status upon being introduced into a new group. Because socioeconomic status in humans is also associated with differences in gene expression, there’s every reason to think that similar effects apply to us.

Friday, May 18, 2012

U.S. Army Major
Jean Muderhwa of the Brooke Army Medical Center/San Antonio Military Medical
Center has developed a ‘microemulsion’ that he hopes will prove useful in
stockpiling vaccines. He presented
his findings at the Experimental Biology 2012 meeting.

An emulsion is a
mixture of liquids that don’t ordinarily mix. The application of energy causes
one liquid to form stable droplets that are dispersed throughout the other
liquid. For example, many cosmetics contain a mixture of oil and water, plus
other ingredients. Milk is an emulsion of butterfat globules and water.
Microemulsions simply contain very tiny droplets that are less than 100 nm across.

Muderhwa’s micoremulsion
is composed of five ingredients: water, oil, glycerol, surfactants (chemicals
that lower the surface tension of liquids making them more ‘mixable’) and a protein
adjuvant, a molecule that makes a body’s response to vaccines more potent. In
other words, the emulsion is specifically designed to carry vaccines.

The system hasn’t been tested for vaccines yet, although microemulsions
are currently used to deliver other kinds of drugs. If all goes well, this new concoction can be used not only for the delivery of vaccines, but also for long term storage until the vaccines are needed.

US Army Major Jean M. Muderhwa's microemulsion vaccine carrier.Courtesy of US Army Major Jean M. Muderhwa

Thursday, May 17, 2012

It was meat-eating that allowed us to advance across the Earth. This is the theory proposed by Elia Psouni from Lund and Kristianstad Universities, Axel Janke from Goethe University and Martin Garwicz from the Neuronano Research Center. According to them, increased meat consumption was the first domino that subsequently led to earlier weaning, increased fertility, more offspring, and finally to world domination. Okay, it’s probably not that simple, but the researchers did find a correlation between meat consumption and time of weaning.

Here’s a comparison with our closest relative, the chimpanzee. About 5% of a chimp’s diet is meat and they wean their babies at around five years old. In contrast, about 20 to 50% of the diet of a modern human hunter-gatherer’s diet is meat and they wean their children at just over two years. Clearly, humans are weaning at a much earlier age. But is this a function of diet or of some other factor?

The scientists compiled information on 67 species of mammal across 12 different orders. Data points included adult female body mass, adult brain mass, time to weaning postnatal and time to weaning post conception. The last attribute represents the total physical investment of the mother. They compared this with data from forty-six human ‘natural fertility societies’ that presumably mimic conditions of the pre-agricultural age.

Regardless of adult size, all species wean their young when the offspring achieve a critical level of brain development. Because of their more nutritious diet, carnivores as a group were able to wean their offspring earlier than herbivores or omnivores.When adjusting for factors such as brain mass, humans wean their children at the same age as other carnivores, rather than when their vegetarian primate cousins wean.

Needless to say, diet is most likely only one of many factors that led to the human migration across the globe. However, weaning does result in a return to fertility for female mammals, so females that wean earlier could have had more babies. It's therefore possible that the shift to meat-eating would have had a profound effect on the number of hominins, and thus on their ability to spread outward.

Tuesday, May 15, 2012

That was the title of a press release I just read. I’m sure the black flies will be delighted to hear this. All this time, they’ve been moping about in existential despair. What, did you think I didn’t write this blog to amuse myself? Okay, obviously, the paper is about how black flies might be of some use to us. So let’s get to it.

Like most biting insects, black flies (Simulium vittatum) secrete products in their saliva to prevent blood from clotting while they’re taking their meal. Hitoshi Tsujimoto and his colleagues from the University of Georgia, the Academy of Sciences of the Czech Republic and from the National Institutes of Health have identified just such a protein in black fly saliva, dubbed ‘Simukunin’. It is expressed only in females but not males, who feed on nectar rather than blood.

Blood clotting in mammals is a complicated business involving a cascade of products. As each protein is cleaved, it becomes the active enzyme capable of cleaving the next in line. Ultimately, the final protein is activated and a fibrin clot is produced. Clotting inhibitors can disrupt the pathway by binding to certain factors and preventing them from cleaving and activating other factors. In this way, coagulation is circumvented.

Sure enough, Simukunin binds to clotting factors and interferes with coagulation. Even more intriguing, Simukunin also appears to play a role in preventing inflammation. It binds even more strongly to factors involved in the inflammatory response.

Because the authors were able to synthesize functional Simukunin, it could prove to be a useful anti-coagulant and possibly anti-inflammatory drug. Black flies can rejoice that they now have meaning in their lives.

By the way, if you want to study black flies you should definitely go to the University of Georgia. They have the only contained black fly colony in the world. Luckily for the residents of Georgia, their flies are not vectors for disease.

Monday, May 14, 2012

Peter Rothwell of the University of Oxford and his colleagues have published two papers outlining the correlation between taking aspirin and not getting cancer. Spoiler alert: you’re going to want to stock up on aspirin. Waiver alert: I’m not a medical doctor. Check with one before starting aspirin therapy.

For one set of experiments, the authors compiled data from five different aspirin trials involving over 17,000 people. The trials were originally conducted to determine the effect of taking aspirin on cardiovascular health, but they contained data on cancer as well. Taking aspirin daily significantly reduced the risk of developing cancer or of having that cancer metastasize to the rest of the body. This was true for lung, liver, bone and brain cancers. The exact mechanism is not known, though it may have something to do with the inhibition of platelet formation.

Daily aspirin was protective even if the person had only been taking it for a few years, and even if the aspirin regimen was started after the person had already been diagnosed with cancer (if the cancer hadn’t already spread throughout the body). How great was the benefit? Metastasis was reduced by up to 40% compared to controls who were not taking aspirin. If the person had started taking aspirin before being diagnosed with cancer, the risk of subsequent metastasis was reduced by 70%.

The second set of experiments, using data from 51 different aspirin trials and over 70,000 people, showed similar results. Twenty-year cancer mortality was decreased by up to 30% in people taking aspirin. After taking aspirin for three years, the risk of getting cancer was decreased by about a quarter.

Taking aspirin is not without risks of its own. In particular, aspirin can increase the risk of major bleeding which, in rare cases, can be fatal. However, that risk diminishes over time. If you’ve taken aspirin safely for three years, you probably don’t have to worry about it anymore. But again, consult a doctor if you’re interested in taking daily aspirin as a prophylactic against cancer or heart disease.

Saturday, May 12, 2012

Katherine Laughon of the National Institutes of Health and her colleagues compared women who gave birth in the sixties to women who gave birth in the naughts (2002 to 2008). The more recent deliveries took about two to three hours longer. I’m sure that’s the last thing anyone contemplating bearing a child wants to hear.

The earlier births were recorded as part of a prospective study called the National Collaborative Perinatal Project (CPP). In contrast, the second group was part of a retrospective study called the Consortium on Safe Labor (CSL). That means that the first group was recruited for the study before going into labor, whereas the second group was asked to remember what had happened some time after the fact. The difference isn’t necessarily that big if there are good records, but in general, prospective studies are considered to be more reliable.

There were some definite differences both in obstetrical practices and in the participants themselves that might have accounted for the change in labor lengths. Compared to the CSL women, the women in the sixties had lower body mass indexes and gave birth to smaller babies. They were far less likely to receive either epidurals or oxytocin and had one quarter as many c-sections. On the plus side, the CSL babies had higher apgar scores (a test of neonatal health).

It’s not clear whether these changes alone were responsible for the longer labors. It may have been a combination of factors or something else entirely. In any case, it’s important that doctors no longer use outmoded guidelines for deciding when it’s time to intervene in labors that don’t seem to be progressing.

Friday, May 11, 2012

Mammals and dinosaurs coexisted for millions of years, but
only mammals (and the branch of dinosaurs known as birds) survive today.
According to Daryl Condon (who is affiliated with three universities
including the University of Zurich) and his colleagues, this may have been
due to their very different reproductive strategies.

Mammals nurture their young internally, whereas dinosaurs
lay eggs, which have a strict upper size limit. A larger egg requires a
thicker sturdier shell. Above a certain thickness, the embryo would no
longer be able to get oxygen through that shell. This means that while a
baby elephant and a baby squirrel can be vastly different in size, newborn
dinosaurs must be much more similar in size. Thus, a mother elephant is about
twenty times as large as her newborn calf, but a similarly sized mother
dinosaur would have been 2500 times larger than her baby.

There are other ramifications of the dinosaur’s oviparous
lifestyle. Mammalian babies tend to eat the same foods as their parents and are
fed milk until they are able to do so. They therefore fill the same ecological
niche as their parents. In contrast, baby dinosaurs might have filled
completely different niches than their parents, and indeed a different niche at
every stage of their development.

In fact, Condon and his colleagues propose that where a given environment could
have supported many different mammalian species, it would have supported only a
single dinosaur species. For example, in one ecosystem, you might have rabbits
eating shrubs, small deer eating leaves from small trees and giraffes eating
the leaves from tall trees. In the same ecosystem, you might have newborn
sauropods eating the shrubs, juveniles eating the leaves of small trees and
adults eating leaves from the tallest trees. All of these niches would have
been filled by a single species. In a similar manner, carnivorous dinosaurs from a single species but different ages might have fed on the different sizes of that sauropod.

This in turn, made the dinosaurs much more
vulnerable to extinction.Suppose one type of plant disappeared from the ecosystem.
Say for some reason, there were no small trees. You’d still have plenty of
mammal species eating other types of plants, but with no juvenile sauropods you’d have
no adults and no new babies either. This might precipitate the end of the dinosaurs from that region.

Obviously, these are oversimplifications. Still Condon and
his colleagues believe this goes a long way to explain why mammals and birds
survived the Cretaceous–Tertiary (K–T) extinction but dinosaurs did not.

Thursday, May 10, 2012

Why are so many people still getting cancer? The unfortunate
answer may be that they caught it from someone else. Let me back track and say
that cancer itself is not contagious. However, many cancers are originally
caused by infectious agents like viruses. How many? Catherine de
Martel and her colleagues from the International Agency for Research on Cancer,
France, estimate that around 16% of all cancers worldwide
began as infections.

Ninety-five percent of those two million new cancer cases
per year are attributable to just four types of viruses: Helicobacter pylori, hepatitis B and C viruses, and human
papillomaviruses. This is actually good news, because we have vaccines against
many of these agents. In fact, vaccination against viral cancers is probably
reflected in the data, since more affluent countries have a far lower rate of
these kinds of cancers. While only about 7% of cancers in developed countries
were caused by infection, 33% of cases in sub-Saharan Africa fell into that
category.

Cancer is considered to be non-communicable, and that’s
still largely true. Not only are the majority of cancers not caused by
infectious agents, but those that are tend to be caused by viruses that are not
that easy to catch. These are not infections you’d get from hugging someone.
Nevertheless, it’s important to recognize the role that viruses play in causing
cancer, and the role that vaccination may play in preventing cancer.

As we
learn more about both cancer and virology, it may be that more cancers with
previously unknown provenance become attributable to viral infection. On
the other hand, Ed Yong, who writes the Not Exactly Rocket Science blog for
Discovery Magazine, points out that the proportion of cancers that result from
infections has not changed for more than a decade.

Wednesday, May 9, 2012

I love videos that make science fun and easy to understand. Here's another offering along that vein, this time from the folks at The Naked Scientist. It's part of their video series called Naked Science Scrapbook.

By the way, The Naked Scientists also produce some excellent podcasts. You can find a link to their website under 'My favorite science podcasts' to the left.

Tuesday, May 8, 2012

Our DNA replication machinery is
remarkably accurate and efficient, but errors do occasionally occur. For
example, the same gene may be replicated more than once, resulting in multiple copies of that gene. According to Evan Eichler and his colleagues from
the University of Washington and other institutions, one such duplication event
may have been responsible for the differences between our brains and those of
the great apes.

The original gene, SRGAP2, encodes a protein that is critical for neuronal
development in mammalian embryos. Around the time Australopithecus was evolving into Homo, we ended up with a couple of extra copies of this gene.
Chimps and orangutans each have only one version of the gene, but we have four.
The first duplication (SRGAP2B) probably occurred about 3.4 million years ago (mya), the
next (SRGAP2C, a copy of SRGAP2B), 2.4 mya, and the last (SRGAP2D, also a copy of SRGAP2B) only 1 mya.

Upon reading that humans have extra copies of a gene involved
in neuron maturation, you might think that it’s the excess amounts of this
protein product that lets us be so brainy. Not so. Franck Polleux of the Scripps Research Institute and his colleagues found that the second SRGAP2 duplication (SRGAP2C) encodes a protein that actually interferes with the original gene product. To operate properly, two SRGAP2 proteins must combine together. Because SRGAP2C encodes an incomplete copy, it can pair with the original SRGAP2, but the result is unusable. In other words, thanks to the duplication events, we have less functional SRGAP2 protein,
not more.

The consequence of this is that the developmental schedule of neurons is
altered. With SRGAP2 blocked
during embryogenesis, the period of time allowed for neuronal development is
elongated. This allows for the formation of longer and more numerous neuronal
spines, the parts of the neuron that make connections with other neurons. SRGAP2 also inhibits neural migration, the spreading of neurons throughout the brain. Without it, neurons can continue to migrate for longer. It’s not difficult to see how these changes would have had a huge impact on the evolution of hominin brains.

Think
about this: not only were there errors in replicating SRGAP2 millions of
years ago, but those errors resulted in a protein product that exactly interfered
with the original product. We may very well owe our ability to reason to those serendipitous events. You gotta love evolution.

Monday, May 7, 2012

If you need a reason to be wary of herbal remedies, take a lesson from the Taiwanese. They’re suffering from the highest rate of upper urinary tract cancer in the world, thanks to Chinese herbal remedies made from the Aristolochia plant (left). Many species of thisplant produce aristolochic acid (AA), a nasty substance that’s a powerful nephrotoxin, meaning it will destroy your kidneys. Now it turns out that AA is a carcinogen as well. Nonetheless, it’s been a component of traditional medicines for centuries.

The connection between AA and kidney failure has been known for decades, but the relationship with certain types of cancer was uncovered by Chung-Hsin Chen of National Taiwan University Hospital and Taoyuan General Hospital and his Taiwanese and American colleagues. They took DNA samples from patients suffering from urinary tract cancer to find that correlation.

The researchers relied on the fact that AA forms long-lasting chemical bonds with DNA. Because of that, specific mutations can be linked to AA exposure. Those same mutations were found in a large majority of the cancer patients, strongly suggesting that the cancers were caused by the ingestion of AA. The fact that one third of all Taiwanese people are known to use remedies containing AA (as estimated from examining the prescription records of 200,000 people) makes it even more likely that the unfortunate study subjects had taken AA. I can only hope that word will get out and people will stop taking these dangerous concoctions.

By the way, think your preferred herbal remedies are safe? Keep in mind that the Food and Drug Administration (FDA) has minimal oversight over herbal remedies. In the case of AA, the best they can do is to ban its import, they have no authority to make sure that remedies don’t contain it. Besides, many herbal products interfere with conventional treatments as Catherine Ulbricht, Senior Attending Pharmacist at Massachusetts General Hospital, describes here.

Stochastic Scientist? What's up with that?

Why the Stochastic Scientist? As I'm sure you all know, 'stochastic' is another word for 'random', which is what I intend for the focus of this blog. Although my formal training is as a molecular biologist, there are many other fields of science that are also fascinating and beautiful. It's my intention to blog about which ever scientific discovery or invention catches my, and hopefully your, fancy.

I also hope to inspire people to learn more about science. By choosing among a huge variety of scientific endeavors, I'll undoubtably hit upon something that will pique my readers' interest.

I guess I could have called my blog 'The Joy of Science', but that wouldn't have been quite so random.